Missing phosphate atom and gap in phosphate backbone

HADDOCK
1

Hi
I am docking a G quadruplex with a protein with Guru level access in Haddock. The G quadruplex has 24 bases with a modified oxo base as G21 named as 8OG(PDB id : 6ia4). The Haddock results shows G21 as separate ligand with no continuous phosphate back bone from A20-G21-G22. Further the G22 base has P atom missing in the PDB coordinate file. In order to keep the G21 in place I have provided the following restraints:
Distance restraints:
assign (segid A and resid 20 and name P)(segid A and resid 20 and name O5’) 1.6 1.6 0.8
assign (segid A and resid 20 and name O5’) (segid A and resid 20 and name C5’) 1.4 1.4 0.8
assign (segid A and resid 20 and name C5’) (segid A and resid 20 and name C4’) 1.5 1.5 0.8
assign (segid A and resid 20 and name C4’) (segid A and resid 20 and name C3’) 1.5 1.5 0.8
assign (segid A and resid 20 and name C3’) (segid A and resid 20 and name O3’) 1.4 1.4 0.8
assign (segid A and resid 20 and name O3’) (segid A and resid 21 and name P) 1.6 1.6 0.8
assign (segid A and resid 21 and name P) (segid A and resid 21 and name O5’) 1.6 1.6 0.8
assign (segid A and resid 21 and name O5’) (segid A and resid 21 and name C5’) 1.4 1.4 0.8
assign (segid A and resid 21 and name C5’) (segid A and resid 21 and name C4’) 1.5 1.5 0.8
assign (segid A and resid 21 and name C4’)(segid A and resid 21 and name C3’) 1.5 1.5 0.8
assign (segid A and resid 21 and name C3’)(segid A and resid 21 and name O3’) 1.4 1.4 0.8
assign (segid A and resid 21 and name O3’)(segid A and resid 22 and name P) 1.6 1.6 0.8
assign (segid A and resid 22 and name P) (segid A and resid 22 and name O5’) 1.6 1.6 0.8
assign (segid A and resid 22 and name O5’) (segid A and resid 22 and name C5’) 1.4 1.4 0.8
assign (segid A and resid 22 and name C5’) (segid A and resid 22 and name C4’) 1.5 1.5 0.8
assign (segid A and resid 22 and name C4’) (segid A and resid 22 and name C3’) 1.5 1.5 0.8
Dihedral restraints:
assign (segid A and resid 20 and name P)(segid A and resid 20 and name O5’)(segid A and resid 20 and name C5’)(segid A and resid 20 and name C4’)
1.0 150.0 40.0 2.0
assign (segid A and resid 20 and name O5’)(segid A and resid 20 and name C5’)(segid A and resid 20 and name C4’)(segid A and resid 20 and name C3’)
1.0 43.0 40.0 2.0
assign (segid A and resid 20 and name C5’)(segid A and resid 20 and name C4’)(segid A and resid 20 and name C3’) (segid A and resid 20 and name O3’)
1.0 133.0 40.0 2.0
assign (segid A and resid 20 and name C4’)(segid A and resid 20 and name C3’) (segid A and resid 20 and name O3’) (segid A and resid 21 and name P) 1.0 -150.0 40.0 2.0
assign (segid A and resid 20 and name C3’) (segid A and resid 20 and name O3’)
(segid A and resid 21 and name P) (segid A and resid 21 and name O5’)1.0 121.0 40.0 2.0
assign (segid A and resid 20 and name O3’) (segid A and resid 21 and name P) (segid A and resid 21 and name O5’) (segid A and resid 21 and name C5’)1.0 -65.0 40.0 2.0
assign (segid A and resid 21 and name P) (segid A and resid 21 and name O5’) (segid A and resid 21 and name C5’) (segid A and resid 21 and name C4’)1.0 150.0 40.0 2.0
assign (segid A and resid 21 and name O5’) (segid A and resid 21 and name C5’) (segid A and resid 21 and name C4’) (segid A and resid 21 and name C3’)1.0 48.0 40.0 2.0
assign (segid A and resid 21 and name C5’) (segid A and resid 21 and name C4’) (segid A and resid 21 and name C3’) (segid A and resid 21 and name O3’)1.0 140.0 40.0 2.0
assign (segid A and resid 21 and name C4’) (segid A and resid 21 and name C3’) (segid A and resid 21 and name O3’) (segid A and resid 22 and name P)1.0 -175.0 40.0 2.0
assign (segid A and resid 21 and name C3’) (segid A and resid 21 and name O3’) (segid A and resid 22 and name P) (segid A and resid 22 and name O5’) 1.0 -82.0 40.0 2.0
assign (segid A and resid 21 and name O3’) (segid A and resid 22 and name P) (segid A and resid 22 and name O5’) (segid A and resid 22 and name C5’) 1.0 -65.0 40.0 2.0
assign (segid A and resid 22 and name P) (segid A and resid 22 and name O5’) (segid A and resid 22 and name C5’) (segid A and resid 22 and name C4’) 1.0 165.0 40.0 2.0
assign (segid A and resid 22 and name O5’) (segid A and resid 22 and name C5’) (segid A and resid 22 and name C4’) (segid A and resid 22 and name C3’) 1.0 57.0 40.0 2.0
assign (segid A and resid 22 and name C5’) (segid A and resid 22 and name C4’) (segid A and resid 22 and name C3’)(segid A and resid 22 and name O3’) 1.0 120.0 40.0 2.0
H bond length:
assign (segid A and resid 3 and name H1) (segid A and resid 21 and name O6) 2.0 2.0 0.8
assign (segid A and resid 3 and name H21) (segid A and resid 21 and name O6) 1.9 1.9 0.8
assign (segid A and resid 17 and name O6) (segid A and resid 21 and name O6) 3.5 3.5 0.8
assign (segid A and resid 17 and name O6) (segid A and resid 21 and name H1) 1.9 1.9 0.8
assign (segid A and resid 17 and name N7) (segid A and resid 21 and name H21) 2.0 2.0 0.8
assign (segid A and resid 20 and name O3’) (segid A and resid 21 and name H22) 2.5 2.5 0.8
assign (segid A and resid 21 and name OP2) (segid A and resid 21 and name H22) 1.9 1.9 0.8
assign (segid A and resid 21 and name O8) (segid A and resid 22 and name O4’) 3.2 3.2 0.8

Still I find that the G21 is taken as a separate ligand and there is a gap in the phosphate backbone.
Why is the P atom missing in the haddock results and how can I put the G21 in place such that I get a continuous phosphate backbone without gap?

2

8OG is simply not supported. Now it is defined as HETATM and as such will not be connected to the remaining of the phosphate backbone.

Still I find that the G21 is taken as a separate ligand and there is a gap in the phosphate backbone.
Why is the P atom missing in the haddock results and how can I put the G21 in place such that I get a continuous phosphate backbone without gap?

For 8OG to be connected we would need to define a new entry for it in our nucleic acid force field, which does require some work.

3

Thank you for the reply.
So does that mean that I will not be currently able to do the docking with the DNA structures having modified bases or
Is it that I have to provide more parameters for docking.

4

As long as this modified base is not supported you can indeed not dock your system properly (or accept that there will be gaps in your backbone)

5

Thank you for the clarification.